Former intelligence contractor Edward Snowden poses for a photo during an interview in an undisclosed location in December in Moscow.

As Edward Snowden prepares to defend himself in a worldwide webinar Thursday, the Justice Department is accusing the private contractor that vetted him and thousands of other intelligence workers of bilking U.S. taxpayers out of tens of millions of dollars by conducting phony background checks.

USIS, the giant private contractor that conducted the background checks of both Snowden and Washington Navy Yard shooter Aaron Alexis, is accused in a Justice Department lawsuit filed Wednesday night of conducting 665,000 fake background checks between 2008 and 2012.

“USIS management devised and executed a scheme to deliberately circumvent contractually required quality reviews of completed background investigations in order to increase the company’s revenues and profits,” said the Justice Department in its complaint, which was filed in U.S. District Court in Alabama.

The DOJ lawsuit cites internal emails to back up charges that USIS senior officials devised a wide-ranging "scheme" to defraud the federal government on background checks through a practice known as "dumping" or "flushing" in order to boost the firm's profits.

"Shelves are as clean as they could get," reads one April 2010 email from a "workload leader" to USIS director of National Quality Assurance. "Flushed everything like a dead goldfish." Another email reads: "Scalping tickets for 'Dick Clark's Dumpin' New Year's Eve!' ... Who needs 2?"

The practice of "dumping" or "flushing" involved certifying to the U.S. Office of Personnel Management that full "quality review" background checks had been performed when in fact those reviews had not been completed. Aided by a software program known as "Blue Zone," USIS identified large volumes of cases at the end of day as "Review Complete" -- and then fraudulently certified them to OPM, according to the complaint.

Between March 2008 and September 2012, "USIS released at least 665,000 background investigations" to OPM, certifying them as completed when they actually hadn’t been, the complaint charges. This amounted to 40 percent of all the background checks performed by USIS done during this period., it said. The allegedly fraudulent background checks included employees seeking security clearances at the Department of Defense, Homeland Security, Justice Department and other federal agencies.

The suit charges that USIS senior management "was fully aware of, and in fact, directed the dumping practices." It notes that the firm was paid $11.7 million in bonuses under its contract between 2008 and 2010.

USIS, which on its website calls itself "the leader in federal background investigations," said in a statement provided to NBC News that "a small group of individuals" was responsible for the bogus checks and that their conduct was "contrary to our values and commitment to exceptional service."

"Since first learning of these allegations nearly two years ago, we have acted decisively to reinforce our processes and management to ensure the quality of our work and adherence to OPM requirements," it said. "We appointed a new leadership team, enhanced oversight procedures, and improved control protocols. From the outset, we have fully cooperated with the government’s investigation and remain focused on delivering the highest quality service under our OPM contracts.”

A company source, who spoke to NBC News on condition of anonymity, said that some employees involved in the fraud "were terminated" and that all of the individuals cited in the complaint — including top USIS executives — no longer work for the firm. The source also stressed that neither the Snowden nor the Alexis background checks were among those cited as fraudulent in the complaint. (The complaint does not identify any of the allegedly improper checks.)

The civil lawsuit was filed by the Justice Department under the False Claims Act. The department adopted claims previously made under seal by Blake Percival, identified as the director of Fieldwork Services at USIS between 2001 and 2011. The suit accuses the company of filing false claims, making false statements and breach of contract.

Percival originally filed a whistleblower lawsuit in 2011 alleging that the Northern Virginia-based firm expedited checks in bulk using the “Blue Zone” software on checks that were never actually performed, according to the DOJ complaint.

Sen. Claire McCaskill, who chairs a Senate panel that has been investigating USIS, said of the Justice complaint highlights the need for legislation requiring tighter oversight of federal contractors performing background checks.

“By now, the stunning failures of this company—and the resulting threats to our national security—are well documented,” she said. "But we can’t wait for the next disaster before tackling something as serious as lapses in protecting our nation’s secrets and our secure facilities.”

A review by U.S. intelligence officials of the 2011 background check of Snowden “revealed several areas of incomplete coverage” resulting in a report “that did not present a comprehensive picture of Mr. Snowden,” according to a copy of an Aug. 23 letter obtained by NBC News that National Counterintelligence Executive Frank Montoya sent to the Office of Personnel Management.

USIS has acknowledged it did the 2011 background check of Snowden as part of a “re-investigation” of him to permit him to retain his high-level security clearance, but said it had been previously told by OPM that “all standards were met.”

After Aaron Alexis shot and killed a dozen people at the Washington Navy Yard on Sept. 16, 2013, USIS acknowledged in a statement that it had also conducted the 2007 background check that allowed him to get a security clearance.

"Today, we were informed that in 2007, USIS conducted a background check of Aaron Alexis” for OPM, USIS spokesman Ray Howell said in a statement emailed to NBC News at the time. "We are contractually prohibited from retaining case information gathered as part of the background checks we conduct for OPM and therefore are unable to comment further on the nature or scope of this or any other background check."

Edward Snowden is scheduled to host a live chat on the web at 3 p.m. ET Thursday, and will be answering questions sent via the Twitter hashtag #asksnowden. The planned webinar is the second public Q&A for Snowden, who answered questions during a June 2013 event hosted by the Guardian and moderated by Glenn Greenwald.